Effective Decontamination for Automated Microbiology Instruments

May 2016 - Vol.5 No. 4 - Page #2
Categories: Cleaning Products, Mass Spectrometry, Materials Handling

The practice of diagnostic microbiology in today’s clinical laboratory is undergoing significant changes. Emerging diagnostic technologies highlighted by fully automated microbiology and molecular-based systems for the rapid detection of infectious diseases, respiratory viruses, gastrointestinal pathogens, and genes that code for antibiotic resistance, have significantly improved and streamlined the laboratory’s ability to identify a wide variety of microbial pathogens in a relatively short period of time compared to traditional methods (ie, minutes and hours versus days).

Undoubtedly, these advances have contributed to increased efficiency and productivity, leading to better patient care, and operational cost-savings, yet it is important that control over instrument and environment safety remain an equal priority. A clinical microbiology lab may contain any number of virulent pathogens at any given time, and though high productivity and efficiency is important, it cannot come at the expense of employee and, ultimately, patient safety. Implementing and refining a chemical decontamination (sterilization) plan for existing and future automation must remain part of a clinical lab’s primary objectives. Fortunately, there are ways in which a modern, automated microbiology lab can achieve full utilization of advanced technologies with efficiency and safety as its governing principles.

Safety and Risk Assessments

Any review of laboratory workplace safety should begin with basic questions related to the conditions under which a piece of instrumentation is currently used, and those under which it ideally should be used. For example:

  • What personnel and environmental safety measures are in place in the event an instrument becomes contaminated with a virulent pathogen as a result of spillage, breakage, aerosolization, splashing, or spraying?
  • Are instrument manufacturer-recommended decontamination guidelines fully incorporated into internal policies and procedures (P&Ps) to ensure the safety of personnel and the laboratory environment?
  • What measures are in place to ensure well-executed P&Ps will effect proper decontamination of instruments and the environment (ie, total sterilization)?

Although each instrument used in the microbiology lab is unique in terms of functionality and the nature of the assay(s) design, from a structural point of view, they tend to share common components: Metal (stainless steel), plastics (housing and tubing), rubber (seals and gaskets), synthetic polyester materials, glass, lubricants, electronics, and robotics (moving parts). While external decontamination is important, and a relatively standard task, the real challenge is complete decontamination of the internal infrastructure and individual components.

Clinical labs must have strict P&Ps in place to manage virulent pathogens, as there is a clear and direct connection between instrument decontamination—specifically, the internal infrastructure—and personnel safety. The primary goals of decontamination are to protect laboratory personnel, the environment, and personnel who enter the laboratory or handle laboratory products away from the laboratory, and render a work area, device, item, or material safe to handle (ie, free from risk of disease).1 Therefore, decontamination efforts must be made to reduce the level of microbial contamination and eliminate transmission of infection, especially laboratory-acquired infections. Environmentally mediated transmission of infection can be enabled directly or indirectly from a variety of environmental sources including air, contaminated fomites, and spillage (resulting from breakage, puncturing of tubing, instrument malfunction, or breaches of instrument integrity). Given this, adherence to best practices for device decontamination and operator safety should be stressed among all staff, and when considering automation acquisitions, the mitigation of contamination and boon to employee safety afforded by such devices should be driving factors.

Click here to see a larger version of FIGURE 1.

With Robotics, Human Error Remains

The robotic nature of fully automated, open and closed microbiology systems is not entirely without risk for contamination from staff and the environment. These systems often consist of a number of activities associated with specimen inoculation, conveyance of culture plates to the incubator, digital photography chambers, and conveyance of plates from the incubator to the technologist’s workstation. Despite built-in and robust safety measures, the potential for breakage, spillage, and aerosolization remains.

Common steps during which contamination can occur include: Opening specimen containers and opening and conveyance of culture plates to the incubator and/or workstation. Sources of robotics-associated contamination include human loading of plates onto the conveyor system, other human interaction with plates during processing, and automated plating of specimens using loops or magnetic beads which are potential sources of aerosols and breakage. Likewise, culture plates could fall from the conveyor and contaminate the surrounding environment. To avoid these scenarios, workplace movement must be disciplined and care should be taken when circumnavigating and interacting with testing automation.

Methods and Effects of Decontamination

Standard, manufacturer-required routine maintenance and cleaning for most automated microbiology devices consists of cleaning (ie, removal of dust, grit, grease) and disinfection with a suitable chemical agent, such as bleach or alcohol. When complete decontamination (sterilization) is required, the choices of methodology and decontaminating agents are often specified, and depending on manufacturer requirements, are supervised by a vendor-appointed, licensed technician.

Due to the size and complexity of larger instruments, such as total laboratory automated systems, decontamination is usually performed on site and may require significant downtime before the system regains full operation. Smaller instruments may be disinfected on site as well, but are usually shipped to the manufacturer for decontamination. This also results in downtime, an attendant loss of revenue, and additional expenditures associated with the temporary outsourcing of testing. These same concepts and concerns apply to MALDI-TOF mass spectrometry technology utilized for the identification of a variety of microorganisms, including biosafety level-3 bio threat agents such as Bacillus anthracis and Yersinia pestis. If colonies of these organisms, along with colonies of Neisseria meningitidis and Brucella species, are not handled properly, they pose a significant exposure risk to laboratory personnel. The question of safety is further highlighted by the questionable effectiveness of currently recommended procedures for microbial inactivation, especially for bacterial spores and prions, which are the most difficult of all microbial forms to inactivate (see FIGURE 1). Although trifluoroacetic acid, used in MALDI-TOF technology, has been demonstrated to be an acceptable method for total inactivation in terms of bactericidal activity, an additional centrifugation and filtration step is recommended to inactivate vegetative organisms and spores.2,3

Managing Sterilization Expectations

It is generally accepted by the scientific community that achieving 100% sterility is probably unrealistic independent of the area, space, or surface (this applies to external and internal infrastructure of instruments). Nonetheless, sterilization can be accomplished using a combination of heat and chemical agents, such as formaldehyde gas/vapor, ethylene oxide, hydrogen peroxide gas/vapor, plasma, ozone, and radiation. All have advantages and disadvantages, but in making a selection, attention must be given to the sensitivity of diagnostic instruments and the impact that the agent may have on instrument function and performance.

Disinfection, which is less lethal than sterilization, kills vegetative organisms but is not as effective against spores or prions. The aforementioned chemical agents, used primarily for sterilization, are generally reserved for decontaminating large spaces, but little or no data is available on their utility in internal decontamination. However, it is common practice to supplement these agents with a pre-cleaning phase prior to their application. When used for external decontamination, they are very effective.

Of these agents, aerosolized or vaporous hydrogen peroxide (VHP) appears to be the most effective and least damaging decontaminating agent due to its effectiveness in eradicating Clostridium difficile, Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), Acinetobacter, viruses, enteric and respiratory pathogens, and demonstrated superior sporicidal activity when compared to other agents.4,5,6,7 VHP has been successfully used to decontaminate equipment in small areas, can be used without disrupting activity or requiring laboratory personnel to be absent from the work area during the decontamination process, is environmentally friendly, and as VHP is converted into oxygen and water vapor, no residue remains at the end of the decontamination cycle. It is worth keeping in mind that while VHP does not appear to damage sensitive and expensive equipment, its effects on the internal components of instruments remains uncertain and requires additional study.


Many questions remain regarding the effectiveness and impact of chemical decontamination (sterilization) agents on highly sensitive clinical laboratory instruments. Science and science-based evidence should dictate decontamination policies for laboratory instruments with an emphasis on a rational, risk-based approach, not a fear- or consequence-based one. Therefore, a partnership is necessary between the scientific community, industry, and applicable government agencies with the expressed purpose of determining the most effective and safe method for the external and internal decontamination of these and future instruments, while ensuring the safety of personnel and the environment. As laboratory managers and practitioners ourselves, we must continue to perform proactive risk assessments, never take safety for granted, be familiar with the currently available decontaminating agents, including their strengths and limitations, and strive to achieve the highest possible level of sterility.


  1. Miller JM, Astles R, Baszler T, et al. Guidelines for safe work practices in human and animal medical diagnostic laboratories. Recommendations of a CDC-convened, Biosafety Blue Ribbon Panel. MMWR Suppl. 2012;61(1):1-102.
  2. Dauphin LA, Bowen MD. A simple method for the rapid removal of Bacillus anthracis spores from DNA preparations. J Microbiol Methods. 2009;76(2):212 – 214.
  3. Lasch P, Nattermann H, Erhard M, et al. MALDI-TOF mass spectrometry compatible inactivation method for highly pathogenic microbial cells and spores. Anal Chem. 2008; 80(6):2026-2034.
  4. Cooper T, O’Leary M, Yezli S, et al. Impact of environmental decontamination using hydrogen peroxide vapour on the incidence of Clostridium difficile infection in one hospital trust. J Hosp Infect. 2011;78(3):238-240.
  5. Falagas ME, Thomaidis PC, Kotsantis IK, et al. Airborne hydrogen peroxide for disinfection of the hospital environment and infection control: a systematic review. J Hosp Infect. 2011; 78(3):171-177.
  6. Tuladhar E, Terpstra P, Koopmans M, et al. Virucidal efficacy of hydrogen peroxide vapour disinfection. J Hosp Infect. 2012;80(2):110-115.
  7. Pottage T, Macken S, Giri K, et al. Low-temperature decontamination with hydrogen peroxide or chlorine dioxide for space applications. Appl Environ Microbiol. 2012;78(12):4169-4174.

James W. Snyder, PhD, D(ABMM), F(AAM), is director of the microbiology and molecular diagnostics (infectious diseases) laboratory at the University of Louisville School of Medicine and Hospital, where he also is a professor of pathology and laboratory medicine (clinical service). Jim earned his PhD in biology (medical microbiology) from the University of Dayton.


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